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Backmerge: #1257 Enhanced stereo labels on atropisomers are lost when opening sa… #1268

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Sep 15, 2023
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Backmerge: #1257 Enhanced stereo labels on atropisomers are lost when opening sa… #1268

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6 changes: 3 additions & 3 deletions api/tests/integration/ref/formats/incorrect_smiles.py.out
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@@ -1,3 +1,3 @@
O[C@H](N)C |&1:0| molecule auto loader: SMILES loader: atom 0 is not a stereocenter
O[C@H](N)C |o1:0| molecule auto loader: SMILES loader: atom 0 is not a stereocenter
O[C@H](N)C |a:3| molecule auto loader: SMILES loader: atom 3 is not a stereocenter
O[C@H](N)C |&1:0| molecule auto loader: stereocenters: stereocenter (0) pyramid must have at least 3 atoms
O[C@H](N)C |o1:0| molecule auto loader: stereocenters: stereocenter (0) pyramid must have at least 3 atoms
O[C@H](N)C |a:3| molecule auto loader: stereocenters: stereocenter (3) pyramid must have at least 3 atoms
1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/mol_to_smiles.py.out
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@@ -1,2 +1,3 @@
C1%82(C%83O%84%85)OC%86(C(O%87%88%89)C(O%90%91)C%921O%93%94%95)O%96%97%98.[*:1]%96.[*:2]%93.[*:3]%84.[*:4]%90.[*:5]%87.[*:6]%94%85.[*:7]%95%97.[*:8]%83.[*:9]%91%88.[*:10]%89%98.[*:11]%86.[*:12]%92.[*:13]%82 |$;;;;;;;;;;;;_R1;_R2;_R3;_R4;_R5;_R6;_R7;_R8;_R9;_R10;_R11;_R12;_R13$|
[O-][N+](C1=NN=NN1CC1N=NNN=1)=O
C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|
3 changes: 3 additions & 0 deletions api/tests/integration/ref/formats/smiles.py.out
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Expand Up @@ -71,3 +71,6 @@ chemaxon:
CCCC |Sg:n:0,1,2::ht|
chemaxon:
CCCCC |Sg:n:1,2,3::hh|
*** Atropisomers ***
atropisomer:
C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4|
7 changes: 7 additions & 0 deletions api/tests/integration/tests/formats/mol_to_smiles.py
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Expand Up @@ -19,3 +19,10 @@
joinPathPy("molecules/1e-0.mol", __file__)
).smiles()
)

indigo.setOption("ignore-stereochemistry-errors", True)
print(
indigo.loadMoleculeFromFile(
joinPathPy("molecules/atropisomer.mol", __file__)
).smiles()
)
6 changes: 6 additions & 0 deletions api/tests/integration/tests/formats/smiles.py
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Expand Up @@ -115,3 +115,9 @@
for sm in mols_smiles:
print("chemaxon:")
print(indigo.loadMolecule(sm).smiles())

print("*** Atropisomers ***")
mols_smiles = ["C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|"]
for sm in mols_smiles:
print("atropisomer:")
print(indigo.loadMolecule(sm).smiles())
3 changes: 3 additions & 0 deletions core/indigo-core/molecule/molecule_stereocenters.h
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Expand Up @@ -82,6 +82,8 @@ namespace indigo
int* getPyramid(int idx);
void setType(int idx, int type, int group);
void setType(int idx, int type);
void setAtropisomeric(int idx, bool val);
bool isAtropisomeric(int idx);
void invertPyramid(int idx);

bool sameGroup(int idx1, int idx2);
Expand Down Expand Up @@ -137,6 +139,7 @@ namespace indigo
// [X, Y, Z, W] -- atom indices or -1 for implicit hydrogen
// (X, Y, Z) go counterclockwise when looking from W.
// if there are pure (implicit) hydrogen, it is W
bool is_atropisomeric = false;
int pyramid[4];
};

Expand Down
1 change: 1 addition & 0 deletions core/indigo-core/molecule/smiles_loader.h
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Expand Up @@ -164,6 +164,7 @@ namespace indigo
void _loadMolecule();
void _parseMolecule();
void _loadParsedMolecule();
void _validateStereoCenters();

void _calcStereocenters();
void _calcCisTrans();
Expand Down
1 change: 1 addition & 0 deletions core/indigo-core/molecule/smiles_saver.h
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Expand Up @@ -128,6 +128,7 @@ namespace indigo
void _writeRingBonds();
void _writeUnsaturated();
void _writeSubstitutionCounts();
void _writeWedges();

bool _shouldWriteAromaticBond(int bond_idx);
void _startExtension();
Expand Down
19 changes: 17 additions & 2 deletions core/indigo-core/molecule/src/molecule_json_loader.cpp
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Expand Up @@ -1107,16 +1107,31 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows)
{
if (mol.stereocenters.getType(sc._atom_idx) == 0)
{
if (!stereochemistry_options.ignore_errors)
if (mol.isAtropisomerismReferenceAtom(sc._atom_idx))
{
mol.stereocenters.add_ignore(mol, sc._atom_idx, sc._type, sc._group, false);
mol.stereocenters.setAtropisomeric(sc._atom_idx, true);
}
else if (stereochemistry_options.ignore_errors)
mol.addStereocentersIgnoreBad(sc._atom_idx, sc._type, sc._group, false); // add non-valid stereocenters
else
throw Error("stereo type specified for atom #%d, but the bond "
"directions does not say that it is a stereocenter",
sc._atom_idx);
mol.addStereocentersIgnoreBad(sc._atom_idx, sc._type, sc._group, false); // add non-valid stereocenters
}
else
mol.stereocenters.setType(sc._atom_idx, sc._type, sc._group);
}

for (int i : mol.edges())
{
if (mol.getBondDirection(i) > 0 && !sensible_bond_directions[i])
{
if (!stereochemistry_options.ignore_errors)
throw Error("direction of bond #%d makes no sense", i);
}
}

MoleculeLayout ml(mol, false);
ml.layout_orientation = UNCPECIFIED;
ml.updateSGroups();
Expand Down
10 changes: 10 additions & 0 deletions core/indigo-core/molecule/src/molecule_stereocenters.cpp
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Expand Up @@ -708,6 +708,16 @@ void MoleculeStereocenters::setType(int idx, int type)
_stereocenters.at(idx).type = type;
}

void MoleculeStereocenters::setAtropisomeric(int idx, bool val)
{
_stereocenters.at(idx).is_atropisomeric = val;
}

bool MoleculeStereocenters::isAtropisomeric(int idx)
{
return _stereocenters.at(idx).is_atropisomeric;
}

const int* MoleculeStereocenters::getPyramid(int idx) const
{
return _stereocenters.at(idx).pyramid;
Expand Down
11 changes: 8 additions & 3 deletions core/indigo-core/molecule/src/molfile_loader.cpp
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Expand Up @@ -2064,7 +2064,10 @@ void MolfileLoader::_postLoad()
if (_bmol->stereocenters.getType(i) == 0)
{
if (_bmol->isAtropisomerismReferenceAtom(i))
{
_bmol->stereocenters.add_ignore(*_bmol, i, _stereocenter_types[i], _stereocenter_groups[i], false);
_bmol->stereocenters.setAtropisomeric(i, true);
}
else if (!stereochemistry_options.ignore_errors)
throw Error("stereo type specified for atom #%d, but the bond "
"directions does not say that it is a stereocenter",
Expand All @@ -2074,10 +2077,12 @@ void MolfileLoader::_postLoad()
_bmol->stereocenters.setType(i, _stereocenter_types[i], _stereocenter_groups[i]);
}

if (!stereochemistry_options.ignore_errors)
for (i = 0; i < _bonds_num; i++)
if (_bmol->getBondDirection(i) > 0 && !_sensible_bond_directions[i])
for (i = 0; i < _bonds_num; i++)
if (_bmol->getBondDirection(i) > 0 && !_sensible_bond_directions[i])
{
if (!stereochemistry_options.ignore_errors)
throw Error("direction of bond #%d makes no sense", i);
}

_bmol->buildCisTrans(_ignore_cistrans.ptr());

Expand Down
78 changes: 53 additions & 25 deletions core/indigo-core/molecule/src/smiles_loader.cpp
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Expand Up @@ -302,28 +302,26 @@ void SmilesLoader::_readOtherStuff()

if (c == 'w') // 'ANY' stereocenters
{
bool skip = true;

// TODO: up/down designators (usually come atom coordinates) -- skipped for now
char wmode = 0;
if (_scanner.lookNext() == 'U')
wmode = 'U';
if (_scanner.lookNext() == 'D')
wmode = 'D';

if (wmode)
_scanner.skip(1);
else if (_scanner.lookNext() == 'D')
_scanner.skip(1);
else
skip = false;

if (_scanner.readChar() != ':')
throw Error("colon expected after 'w'");
throw Error("colon expected after 'w%c'", wmode);

while (isdigit(_scanner.lookNext()))
{
int idx = _scanner.readUnsigned();

if (!skip)
int atom_idx = _scanner.readUnsigned();
if (!wmode)
{
// This either bond can mark stereocenter or cis-trans double bond
// For example CC=CN |w:1.0|
const Vertex& v = _bmol->getVertex(idx);
const Vertex& v = _bmol->getVertex(atom_idx);
bool found = false;
for (int nei : v.neighbors())
{
Expand All @@ -337,25 +335,41 @@ void SmilesLoader::_readOtherStuff()

if (!found)
{
if (!_bmol->isPossibleStereocenter(idx))
if (!_bmol->isPossibleStereocenter(atom_idx))
{
if (!stereochemistry_options.ignore_errors)
throw Error("chirality not possible on atom #%d", idx);
throw Error("chirality not possible on atom #%d", atom_idx);
}
else
{
// Check if the stereocenter has already been marked as any
// For example [H]C1(O)c2ccnn2[C@@H](O)c2ccnn12 |r,w:1.0,1.1|
if (_bmol->stereocenters.getType(idx) != MoleculeStereocenters::ATOM_ANY)
_bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_ANY, 0, false);
if (_bmol->stereocenters.getType(atom_idx) != MoleculeStereocenters::ATOM_ANY)
_bmol->addStereocenters(atom_idx, MoleculeStereocenters::ATOM_ANY, 0, false);
}
}
}

if (_scanner.lookNext() == '.') // skip the bond index
if (_scanner.lookNext() == '.')
{
_scanner.skip(1);
_scanner.readUnsigned();
auto bond_idx = _scanner.readUnsigned();
if (wmode)
{
auto& v = _bmol->getEdge(bond_idx);
if (v.end == atom_idx)
_bmol->swapEdgeEnds(bond_idx);
if (v.beg == atom_idx)
{
_bmol->setBondDirection(bond_idx, wmode == 'U' ? BOND_UP : BOND_DOWN);
if (_bmol->isAtropisomerismReferenceAtom(atom_idx))
{
if (!_bmol->stereocenters.exists(atom_idx))
_bmol->addStereocenters(atom_idx, MoleculeStereocenters::ATOM_ANY, 0, false);
_bmol->stereocenters.setAtropisomeric(atom_idx, true);
}
}
}
}

if (_scanner.lookNext() == ',')
Expand All @@ -376,8 +390,8 @@ void SmilesLoader::_readOtherStuff()
_bmol->stereocenters.setType(idx, MoleculeStereocenters::ATOM_ABS, 0);
_overtly_defined_abs.insert(idx);
}
else if (!stereochemistry_options.ignore_errors)
throw Error("atom %d is not a stereocenter", idx);
else
_bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_ABS, 0, false);

if (_scanner.lookNext() == ',')
_scanner.skip(1);
Expand All @@ -396,8 +410,8 @@ void SmilesLoader::_readOtherStuff()

if (_bmol->stereocenters.exists(idx))
_bmol->stereocenters.setType(idx, MoleculeStereocenters::ATOM_OR, groupno);
else if (!stereochemistry_options.ignore_errors)
throw Error("atom %d is not a stereocenter", idx);
else
_bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_OR, groupno, false);

if (_scanner.lookNext() == ',')
_scanner.skip(1);
Expand All @@ -413,11 +427,10 @@ void SmilesLoader::_readOtherStuff()
while (isdigit(_scanner.lookNext()))
{
int idx = _scanner.readUnsigned();

if (_bmol->stereocenters.exists(idx))
_bmol->stereocenters.setType(idx, MoleculeStereocenters::ATOM_AND, groupno);
else if (!stereochemistry_options.ignore_errors)
throw Error("atom %d is not a stereocenter", idx);
else
_bmol->addStereocenters(idx, MoleculeStereocenters::ATOM_AND, groupno, false);

if (_scanner.lookNext() == ',')
_scanner.skip(1);
Expand Down Expand Up @@ -1327,6 +1340,20 @@ void SmilesLoader::_readOtherStuff()
_bmol->removeAtoms(to_remove);
}

void SmilesLoader::_validateStereoCenters()
{
for (int i = _bmol->stereocenters.begin(); i < _bmol->stereocenters.end(); i = _bmol->stereocenters.next(i))
{
auto atom_idx = _bmol->stereocenters.getAtomIndex(i);
if (_bmol->isPossibleStereocenter(atom_idx) || _bmol->isAtropisomerismReferenceAtom(atom_idx))
continue;
if (stereochemistry_options.ignore_errors)
_bmol->stereocenters.remove(i);
else
throw Error("atom %d is not a stereocenter", atom_idx);
}
}

void SmilesLoader::loadSMARTS(QueryMolecule& mol)
{
mol.clear();
Expand Down Expand Up @@ -2412,6 +2439,7 @@ void SmilesLoader::_loadMolecule()

_parseMolecule();
_loadParsedMolecule();
_validateStereoCenters();
}

void SmilesLoader::_readBond(Array<char>& bond_str, _BondDesc& bond, std::unique_ptr<QueryMolecule::Bond>& qbond)
Expand Down
35 changes: 34 additions & 1 deletion core/indigo-core/molecule/src/smiles_saver.cpp
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Expand Up @@ -262,7 +262,7 @@ void SmilesSaver::_saveMolecule()

stereocenters.get(i, atom_idx, type, group, pyramid);

if (type < MoleculeStereocenters::ATOM_AND)
if (type < MoleculeStereocenters::ATOM_AND || stereocenters.isAtropisomeric(atom_idx))
continue;

int implicit_h_idx = -1;
Expand Down Expand Up @@ -625,6 +625,7 @@ void SmilesSaver::_saveMolecule()
_writeRingBonds();
_writeUnsaturated();
_writeSubstitutionCounts();
_writeWedges();

if (_comma)
_output.writeChar('|');
Expand Down Expand Up @@ -1836,6 +1837,38 @@ void SmilesSaver::_writeSubstitutionCounts()
}
}

void SmilesSaver::_writeWedges()
{
bool is_first = true;

if (_bmol)
{
for (int i = 0; i < _written_bonds.size(); ++i)
{
auto bond_idx = _written_bonds[i];
auto& e = _bmol->getEdge(bond_idx);
if (_bmol->stereocenters.exists(e.beg) && _bmol->stereocenters.isAtropisomeric(e.beg))
{
auto bdir = _bmol->getBondDirection(bond_idx);
if (bdir && bdir < BOND_EITHER)
{
if (is_first)
{
_startExtension();
_output.writeString(bdir == BOND_UP ? "wU:" : "wD:");
is_first = false;
}
else
_output.writeString(",");
const auto& edge = _bmol->getEdge(bond_idx);
auto wa_idx = _written_atoms.find(edge.beg);
_output.printf("%d.%d", wa_idx, i);
}
}
}
}
}

void SmilesSaver::_writeRingBonds()
{
bool is_first = true;
Expand Down
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